MK5 Microarray Data

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.

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Filtered	Gene	Value Type	description	Rank	Network Comparison Type	network_comparison	Interaction Map	green	red

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Showing element 551 to 600 of 77072 in total

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Value Type  : Measured

description	Rank	Network Comparison Type	network_comparison	Interaction Map	green	red
cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	155	Divided	1.26273	Low confidence	5341.81	4230.36
	166		1.2611	High confidence	7099.51	5629.62
cytochrome c oxidase polypeptide viia-heart, mitochondrial precursor (ec 1.9.3.1) (cytochrome c oxidase subunit viia-h) (cox viia-m). [swissprot;acc:p24310]	510	Subtracted	70.54	Low confidence	1284.05	1354.59
	535	Divided	1.05494
cytochrome c oxidase polypeptide viic, mitochondrial precursor (ec 1.9.3.1). [swissprot;acc:p15954]	29	Subtracted	582.8		21088.5	20505.7
	637	Divided	1.02842
cytochrome c oxidase subunit viia-l related protein, mitochondrial precursor. [swissprot;acc:o60397]	508	Subtracted	72.14		1279.26	1351.4
	518	Divided	1.05639
cytochrome p450 3a7 (ec 1.14.14.1) (cypiiia7) (p450-hfla). [swissprot;acc:p24462]	334	Subtracted	146.1		2467.83	2321.73
	488	Divided	1.06293
cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [swissprot;acc:q9hbi6]	147		1.29455	High confidence	378.206	292.152
	234	Subtracted	239.61	Low confidence	2368.14	2128.53
	307		86.054	High confidence	378.206	292.152
	384	Divided	1.11257	Low confidence	2368.14	2128.53
cytochrome p450 4f12 (ec 1.14.14.1) (cypivf12). [swissprot;acc:q9hcs2]	146		1.29466	High confidence	377.574	291.639
	233	Subtracted	240.99	Low confidence	2387.52	2146.53
	308		85.935	High confidence	377.574	291.639
	387	Divided	1.11227	Low confidence	2387.52	2146.53
cytochrome p450 4f2 (ec 1.14.13.30) (cypivf2) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:p78329]	149		1.29435	High confidence	379.474	293.178
	235	Subtracted	239.23	Low confidence	2352.74	2113.51
	306		86.296	High confidence	379.474	293.178
	383	Divided	1.11319	Low confidence	2352.74	2113.51
cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [swissprot;acc:p98187]	148		1.29435	High confidence	379.474	293.178
	230	Subtracted	243.18	Low confidence	2407.52	2164.34
	305		86.296	High confidence	379.474	293.178
	386	Divided	1.11236	Low confidence	2407.52	2164.34
cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452]	125		1.33333		56	42
	132			High confidence
	445	Subtracted	14
	773			Low confidence
daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959]	114	Divided	1.4204	High confidence	472.945	671.769
	167	Subtracted	198.824
	571		55.09	Low confidence	4400.61	4455.7
	749	Divided	1.01252
dc11 protein. [refseq;acc:nm_020186]	173		1.22482		681	556
	180			High confidence
	254	Subtracted	125
	386			Low confidence
dead (asp-glu-ala-asp) box polypeptide 47; hqp0256 protein. [refseq;acc:nm_016355]	321		156.08		2083.09	1927.01
	327	Divided	1.09034	High confidence	161.091	175.644
	438	Subtracted	14.553
	445	Divided	1.081	Low confidence	2083.09	1927.01
dead-box protein 3, y-chromosomal. [swissprot;acc:o15523]	360	Subtracted	136.07		2301.01	2437.08
	506	Divided	1.05913
dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9]	32	Subtracted	550.54		3026.64	2476.1
	109	Divided	1.44	High confidence	144	100
	175		1.22234	Low confidence	3026.64	2476.1
	374	Subtracted	44	High confidence	144	100
dead-box protein. [refseq;acc:nm_018665]	76	Divided	1.71403		183	313.667
	243	Subtracted	130.667

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
- Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
- Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
- Filtered specifies whether we only included the high confidence microarry measurements or not.